[gammon:~/sct] barryrl% ./install_sct Welcome to the SCT installer! SCT version ......... dev Installation type ... in-place Operating system .... osx sudo mode ........... 0 To improve user experience and fix bugs, the SCT development team is using a report system to automatically receive crash reports and errors from users. These reports are anonymous. Do you agree to help us improve SCT? [y]es/[n]o: y ./install_sct: line 290: spinalcordtoolbox/sentry_dsn.py: Permission denied --> Crash reports will be sent to the SCT development team. Thank you! -tcsh SCT will be installed here: [/Users/barryrl/sct] Do you agree? [y]es/[n]o: n Choose install directory. Warning! Give full path (e.g. /usr/django/sct_v3.0): /Applications/SCT/ver_4_0_0_beta_2 Copying source files from /Users/barryrl/sct to /Applications/SCT/ver_4_0_0_beta_2 .................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................. Installing conda... >> rm -rf /Applications/SCT/ver_4_0_0_beta_2/python >> mkdir -p /Applications/SCT/ver_4_0_0_beta_2/python % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 20.3M 100 20.3M 0 0 24.7M 0 --:--:-- --:--:-- --:--:-- 24.7M exit status is 0 >> bash /var/folders/mf/5wv63z61295dcfvzm_l2llh8003jn9/T/tmp.WkqmSOyt/miniconda.sh -p /Applications/SCT/ver_4_0_0_beta_2/python -b -f PREFIX=/Applications/SCT/ver_4_0_0_beta_2/python installing: python-2.7.12-1 ... installing: conda-env-2.5.2-py27_0 ... installing: openssl-1.0.2h-1 ... installing: pycosat-0.6.1-py27_1 ... installing: pyyaml-3.11-py27_4 ... installing: readline-6.2-2 ... installing: requests-2.10.0-py27_0 ... installing: ruamel_yaml-0.11.14-py27_0 ... installing: sqlite-3.13.0-0 ... installing: tk-8.5.18-0 ... installing: yaml-0.1.6-0 ... installing: zlib-1.2.8-3 ... installing: conda-4.1.11-py27_0 ... installing: pycrypto-2.6.1-py27_4 ... installing: pip-8.1.2-py27_0 ... installing: wheel-0.29.0-py27_0 ... installing: setuptools-23.0.0-py27_0 ... Python 2.7.12 :: Continuum Analytics, Inc. creating default environment... using -f (force) option installation finished. Conda installation successful >> . /Applications/SCT/ver_4_0_0_beta_2/python/bin/activate /Applications/SCT/ver_4_0_0_beta_2/python Fetching package metadata ....... Solving package specifications: .......... Package plan for installation in environment /Applications/SCT/ver_4_0_0_beta_2/python: The following packages will be downloaded: package | build ---------------------------|----------------- conda-env-2.6.0 | 0 601 B asn1crypto-0.22.0 | py27_0 145 KB enum34-1.1.6 | py27_0 54 KB idna-2.6 | py27_0 122 KB ipaddress-1.0.18 | py27_0 30 KB pycparser-2.18 | py27_0 166 KB pyparsing-2.2.0 | py27_0 93 KB pytz-2017.2 | py27_0 203 KB requests-2.14.2 | py27_0 701 KB six-1.10.0 | py27_0 16 KB cffi-1.10.0 | py27_0 195 KB clyent-1.2.2 | py27_0 15 KB packaging-16.8 | py27_0 29 KB python-dateutil-2.6.1 | py27_0 236 KB anaconda-client-1.6.3 | py27_0 129 KB cryptography-1.8.1 | py27_0 468 KB pyopenssl-17.0.0 | py27_0 73 KB conda-4.3.30 | py27h407ed3a_0 507 KB ------------------------------------------------------------ Total: 3.1 MB The following NEW packages will be INSTALLED: anaconda-client: 1.6.3-py27_0 asn1crypto: 0.22.0-py27_0 cffi: 1.10.0-py27_0 clyent: 1.2.2-py27_0 cryptography: 1.8.1-py27_0 enum34: 1.1.6-py27_0 idna: 2.6-py27_0 ipaddress: 1.0.18-py27_0 packaging: 16.8-py27_0 pycparser: 2.18-py27_0 pyopenssl: 17.0.0-py27_0 pyparsing: 2.2.0-py27_0 python-dateutil: 2.6.1-py27_0 pytz: 2017.2-py27_0 six: 1.10.0-py27_0 The following packages will be UPDATED: conda: 4.1.11-py27_0 --> 4.3.30-py27h407ed3a_0 conda-env: 2.5.2-py27_0 --> 2.6.0-0 requests: 2.10.0-py27_0 --> 2.14.2-py27_0 Fetching packages ... conda-env-2.6. 100% |################################################################| Time: 0:00:00 713.90 kB/s asn1crypto-0.2 100% |################################################################| Time: 0:00:00 17.90 MB/s enum34-1.1.6-p 100% |################################################################| Time: 0:00:00 16.74 MB/s idna-2.6-py27_ 100% |################################################################| Time: 0:00:00 15.05 MB/s ipaddress-1.0. 100% |################################################################| Time: 0:00:00 13.16 MB/s pycparser-2.18 100% |################################################################| Time: 0:00:00 17.42 MB/s pyparsing-2.2. 100% |################################################################| Time: 0:00:00 17.70 MB/s pytz-2017.2-py 100% |################################################################| Time: 0:00:00 14.65 MB/s requests-2.14. 100% |################################################################| Time: 0:00:00 26.35 MB/s six-1.10.0-py2 100% |################################################################| Time: 0:00:00 8.71 MB/s cffi-1.10.0-py 100% |################################################################| Time: 0:00:00 16.75 MB/s clyent-1.2.2-p 100% |################################################################| Time: 0:00:00 8.60 MB/s packaging-16.8 100% |################################################################| Time: 0:00:00 15.69 MB/s python-dateuti 100% |################################################################| Time: 0:00:00 16.67 MB/s anaconda-clien 100% |################################################################| Time: 0:00:00 12.63 MB/s cryptography-1 100% |################################################################| Time: 0:00:00 19.29 MB/s pyopenssl-17.0 100% |################################################################| Time: 0:00:00 13.56 MB/s conda-4.3.30-p 100% |################################################################| Time: 0:00:00 21.57 MB/s Extracting packages ... [ COMPLETE ]|###################################################################################| 100% Unlinking packages ... [ COMPLETE ]|###################################################################################| 100% Linking packages ... [ COMPLETE ]|###################################################################################| 100% Installing Python dependencies... Fetching package metadata ............. Solving package specifications: . Package plan for installation in environment /Applications/SCT/ver_4_0_0_beta_2/python: The following NEW packages will be INSTALLED: backports: 1.0-py_2 conda-forge backports.functools_lru_cache: 1.5-py_1 conda-forge backports.weakref: 1.0rc1-py27_1 conda-forge backports_abc: 0.5-py_1 conda-forge blas: 1.1-openblas conda-forge bleach: 1.5.0-py27_0 conda-forge ca-certificates: 2019.3.9-hecc5488_0 conda-forge certifi: 2019.3.9-py27_0 conda-forge chardet: 3.0.4-py27_1003 conda-forge cloudpickle: 0.8.1-py_0 conda-forge cycler: 0.10.0-py_1 conda-forge cytoolz: 0.9.0.1-py27h1de35cc_1001 conda-forge dask-core: 1.2.0-py_0 conda-forge decorator: 4.4.0-py_0 conda-forge freetype: 2.10.0-h24853df_0 conda-forge funcsigs: 1.0.2-py_3 conda-forge functools32: 3.2.3.2-py_3 conda-forge futures: 3.2.0-py27_1000 conda-forge html5lib: 0.9999999-py27_0 conda-forge imageio: 2.5.0-py27_0 conda-forge intel-openmp: 2019.3-199 jpeg: 9c-h1de35cc_1001 conda-forge kiwisolver: 1.0.1-py27h04f5b5a_1002 conda-forge libblas: 3.8.0-5_hd44dcd8_netlib conda-forge libcblas: 3.8.0-5_hd44dcd8_netlib conda-forge libcxx: 8.0.0-2 conda-forge libcxxabi: 8.0.0-2 conda-forge libgfortran: 3.0.1-0 conda-forge liblapack: 3.8.0-5_hd44dcd8_netlib conda-forge libpng: 1.6.37-h2573ce8_0 conda-forge libprotobuf: 3.7.1-hfbae3c0_0 conda-forge libtiff: 4.0.10-h79f4b77_1001 conda-forge markdown: 2.6.11-py_0 conda-forge matplotlib: 2.2.3-py27_1 conda-forge matplotlib-base: 2.2.3-py27hd64abcd_1 conda-forge mkl: 2018.0.3-1 mkl-service: 1.1.2-py27h6b9c3cc_4 mock: 2.0.0-py27_1001 conda-forge networkx: 2.2-py_1 conda-forge numpy: 1.11.3-py27_blas_openblas_201 conda-forge [blas_openblas] olefile: 0.46-py_0 conda-forge openblas: 0.2.18-6 conda-forge pandas: 0.23.4-py27h1702cab_1000 conda-forge pbr: 5.1.3-py_0 conda-forge pillow: 6.0.0-py27h7095ceb_0 conda-forge protobuf: 3.7.1-py27h6de7cb9_0 conda-forge psutil: 5.6.1-py27h1de35cc_0 conda-forge pyqt: 4.11.4-py27_2 conda-forge pysocks: 1.6.8-py27_1002 conda-forge pywavelets: 1.0.3-py27h1e5eb4f_1 conda-forge qt: 4.8.7-1 scikit-image: 0.14.2-py27h0a44026_1 conda-forge scikit-learn: 0.17.1-np111py27_blas_openblas_202 conda-forge [blas_openblas] scipy: 1.2.1-py27hbd7caa9_1 conda-forge singledispatch: 3.4.0.3-py27_1000 conda-forge sip: 4.18-py27_1 conda-forge subprocess32: 3.5.3-py27h470a237_0 conda-forge tensorflow: 1.3.0-py27_0 conda-forge toolz: 0.9.0-py_1 conda-forge tornado: 5.1.1-py27h1de35cc_1000 conda-forge urllib3: 1.24.1-py27_1000 conda-forge webencodings: 0.5.1-py_1 conda-forge werkzeug: 0.15.2-py_0 conda-forge xlrd: 1.2.0-py_0 conda-forge xlutils: 2.0.0-py27_1 xlwt: 1.3.0-py_1 conda-forge xz: 5.2.4-h1de35cc_1001 conda-forge The following packages will be UPDATED: conda: 4.3.30-py27h407ed3a_0 --> 4.6.12-py27_2 conda-forge conda-env: 2.6.0-0 --> 2.6.0-1 conda-forge cryptography: 1.8.1-py27_0 --> 2.6.1-py27h212c5bf_0 conda-forge openssl: 1.0.2h-1 --> 1.1.1b-h01d97ff_2 conda-forge pip: 8.1.2-py27_0 --> 19.0.3-py27_0 conda-forge pycosat: 0.6.1-py27_1 --> 0.6.3-py27h1de35cc_1001 conda-forge requests: 2.14.2-py27_0 --> 2.21.0-py27_1000 conda-forge setuptools: 23.0.0-py27_0 --> 41.0.0-py27_0 conda-forge tk: 8.5.18-0 --> 8.6.9-ha441bb4_1001 conda-forge zlib: 1.2.8-3 --> 1.2.11-h1de35cc_1004 conda-forge The following packages will be DOWNGRADED: python: 2.7.12-1 --> 2.7.3-5 ca-certificate 100% |################################################################| Time: 0:00:00 20.76 MB/s conda-env-2.6. 100% |################################################################| Time: 0:00:00 2.19 MB/s intel-openmp-2 100% |################################################################| Time: 0:00:00 28.02 MB/s jpeg-9c-h1de35 100% |################################################################| Time: 0:00:00 34.69 MB/s libcxxabi-8.0. 100% |################################################################| Time: 0:00:00 37.18 MB/s libgfortran-3. 100% |################################################################| Time: 0:00:00 15.81 MB/s xz-5.2.4-h1de3 100% |################################################################| Time: 0:00:00 28.71 MB/s zlib-1.2.11-h1 100% |################################################################| Time: 0:00:00 37.68 MB/s libblas-3.8.0- 100% |################################################################| Time: 0:00:00 47.08 MB/s libcxx-8.0.0-2 100% |################################################################| Time: 0:00:00 35.88 MB/s libpng-1.6.37- 100% |################################################################| Time: 0:00:00 38.30 MB/s mkl-2018.0.3-1 100% |################################################################| Time: 0:00:04 34.51 MB/s openblas-0.2.1 100% |################################################################| Time: 0:00:00 35.82 MB/s openssl-1.1.1b 100% |################################################################| Time: 0:00:00 41.05 MB/s python-2.7.3-5 100% |################################################################| Time: 0:00:00 45.31 MB/s tk-8.6.9-ha441 100% |################################################################| Time: 0:00:00 42.89 MB/s backports-1.0- 100% |################################################################| Time: 0:00:00 3.39 MB/s backports_abc- 100% |################################################################| Time: 0:00:00 5.06 MB/s blas-1.1-openb 100% |################################################################| Time: 0:00:00 903.67 kB/s certifi-2019.3 100% |################################################################| Time: 0:00:00 37.61 MB/s chardet-3.0.4- 100% |################################################################| Time: 0:00:00 39.69 MB/s cloudpickle-0. 100% |################################################################| Time: 0:00:00 10.82 MB/s dask-core-1.2. 100% |################################################################| Time: 0:00:00 35.72 MB/s decorator-4.4. 100% |################################################################| Time: 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Time: 0:00:00 27.76 MB/s markdown-2.6.1 100% |################################################################| Time: 0:00:00 24.61 MB/s mkl-service-1. 100% |################################################################| Time: 0:00:00 6.90 MB/s olefile-0.46-p 100% |################################################################| Time: 0:00:00 11.27 MB/s psutil-5.6.1-p 100% |################################################################| Time: 0:00:00 37.02 MB/s pycosat-0.6.3- 100% |################################################################| Time: 0:00:00 31.13 MB/s pysocks-1.6.8- 100% |################################################################| Time: 0:00:00 20.45 MB/s sip-4.18-py27_ 100% |################################################################| Time: 0:00:00 45.24 MB/s subprocess32-3 100% |################################################################| Time: 0:00:00 19.95 MB/s toolz-0.9.0-py 100% 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numpy-1.11.3-p 100% |################################################################| Time: 0:00:00 35.03 MB/s pillow-6.0.0-p 100% |################################################################| Time: 0:00:00 50.21 MB/s qt-4.8.7-1.tar 100% |################################################################| Time: 0:00:02 20.44 MB/s setuptools-41. 100% |################################################################| Time: 0:00:00 24.25 MB/s singledispatch 100% |################################################################| Time: 0:00:00 13.35 MB/s xlutils-2.0.0- 100% |################################################################| Time: 0:00:00 17.26 MB/s backports.func 100% |################################################################| Time: 0:00:00 5.32 MB/s bleach-1.5.0-p 100% |################################################################| Time: 0:00:00 14.44 MB/s cryptography-2 100% |################################################################| Time: 0:00:00 30.62 MB/s imageio-2.5.0- 100% |################################################################| Time: 0:00:00 26.28 MB/s networkx-2.2-p 100% |################################################################| Time: 0:00:00 22.17 MB/s pandas-0.23.4- 100% |################################################################| Time: 0:00:00 21.87 MB/s pip-19.0.3-py2 100% |################################################################| Time: 0:00:00 27.75 MB/s protobuf-3.7.1 100% |################################################################| Time: 0:00:00 18.59 MB/s pyqt-4.11.4-py 100% |################################################################| Time: 0:00:00 16.58 MB/s pywavelets-1.0 100% |################################################################| Time: 0:00:00 26.40 MB/s scipy-1.2.1-py 100% |################################################################| Time: 0:00:00 24.22 MB/s tornado-5.1.1- 100% |################################################################| Time: 0:00:00 27.99 MB/s matplotlib-bas 100% |################################################################| Time: 0:00:00 38.74 MB/s pbr-5.1.3-py_0 100% |################################################################| Time: 0:00:00 26.91 MB/s scikit-learn-0 100% |################################################################| Time: 0:00:00 33.06 MB/s matplotlib-2.2 100% |################################################################| Time: 0:00:00 6.18 MB/s mock-2.0.0-py2 100% |################################################################| Time: 0:00:00 50.49 MB/s scikit-image-0 100% |################################################################| Time: 0:00:00 46.50 MB/s urllib3-1.24.1 100% |################################################################| Time: 0:00:00 45.72 MB/s requests-2.21. 100% |################################################################| Time: 0:00:00 27.53 MB/s tensorflow-1.3 100% |################################################################| Time: 0:00:00 37.10 MB/s conda-4.6.12-p 100% |################################################################| Time: 0:00:00 45.93 MB/s /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7. Obtaining file:///Applications/SCT/ver_4_0_0_beta_2 Collecting Keras (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/5e/10/aa32dad071ce52b5502266b5c659451cfd6ffcbf14e6c8c4f16c0ff5aaab/Keras-2.2.4-py2.py3-none-any.whl (312kB) 100% |████████████████████████████████| 317kB 10.8MB/s Collecting dipy (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/e1/30/f1b41ecf027429bc8d714c776f40690ce1d3f28e891f061fe5617ce8b8bf/dipy-0.16.0.tar.gz (11.4MB) 100% |████████████████████████████████| 11.4MB 1.7MB/s Requirement already satisfied: futures in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (3.2.0) Collecting h5py (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/98/06/0e711ae0c95d92ec238218448a15c23590cb117ded59e4bfa322b085b59e/h5py-2.9.0-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (6.1MB) 100% |████████████████████████████████| 6.1MB 2.2MB/s Requirement already satisfied: matplotlib in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.2.3) Collecting nibabel (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/bc/d4/64957ef575ac6b47d02f7195347e3444538ab633460ff6e99d2acc304223/nibabel-2.4.0-py2-none-any.whl (3.3MB) 100% |████████████████████████████████| 3.3MB 6.7MB/s Collecting nipy (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/ed/7f/c4e27b1701ce1fc86cfe7c75c981ccab9be30f38dd409dcc2b1a50c0b4e2/nipy-0.4.2-cp27-cp27m-macosx_10_6_intel.macosx_10_9_intel.macosx_10_9_x86_64.macosx_10_10_intel.macosx_10_10_x86_64.whl (3.6MB) 100% |████████████████████████████████| 3.6MB 6.6MB/s Requirement already satisfied: pandas in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.23.4) Requirement already satisfied: psutil in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (5.6.1) Collecting raven (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/bd/8e/62e26a88c0a1bbae677200baf0767c1022321a6555634f8129e6d55c5ddc/raven-6.10.0-py2.py3-none-any.whl (284kB) 100% |████████████████████████████████| 286kB 8.7MB/s Requirement already satisfied: requests in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.21.0) Requirement already satisfied: numpy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.11.3) Requirement already satisfied: scipy in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.1) Requirement already satisfied: scikit-image in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.14.2) Requirement already satisfied: scikit-learn==0.17.1 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (0.17.1) Requirement already satisfied: tensorflow==1.3.0 in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0) Requirement already satisfied: xlrd in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.2.0) Requirement already satisfied: xlutils in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (2.0.0) Requirement already satisfied: xlwt in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.3.0) Collecting tqdm (from spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/6c/4b/c38b5144cf167c4f52288517436ccafefe9dc01b8d1c190e18a6b154cd4a/tqdm-4.31.1-py2.py3-none-any.whl (48kB) 100% |████████████████████████████████| 51kB 9.3MB/s Collecting transforms3d (from spinalcordtoolbox===dev) Requirement already satisfied: urllib3[secure] in ./python/lib/python2.7/site-packages (from spinalcordtoolbox===dev) (1.24.1) Collecting portalocker (from spinalcordtoolbox===dev) Using cached https://files.pythonhosted.org/packages/eb/48/bf5e330d7d6d57d92157480db9ccad84da86efd045205f7133a53b29aace/portalocker-1.4.0-py2.py3-none-any.whl Collecting keras-applications>=1.0.6 (from Keras->spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/90/85/64c82949765cfb246bbdaf5aca2d55f400f792655927a017710a78445def/Keras_Applications-1.0.7-py2.py3-none-any.whl (51kB) 100% |████████████████████████████████| 61kB 21.6MB/s Requirement already satisfied: pyyaml in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (3.11) Collecting keras-preprocessing>=1.0.5 (from Keras->spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/c0/bf/0315ef6a9fd3fc2346e85b0ff1f5f83ca17073f2c31ac719ab2e4da0d4a3/Keras_Preprocessing-1.0.9-py2.py3-none-any.whl (59kB) 100% |████████████████████████████████| 61kB 23.7MB/s Requirement already satisfied: six>=1.9.0 in ./python/lib/python2.7/site-packages (from Keras->spinalcordtoolbox===dev) (1.10.0) Requirement already satisfied: cycler>=0.10 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (0.10.0) Requirement already satisfied: pyparsing!=2.0.4,!=2.1.2,!=2.1.6,>=2.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.2.0) Requirement already satisfied: python-dateutil>=2.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2.6.1) Requirement already satisfied: pytz in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (2017.2) Requirement already satisfied: kiwisolver>=1.0.1 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.0.1) Requirement already satisfied: backports.functools_lru_cache in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (1.5) Requirement already satisfied: subprocess32 in ./python/lib/python2.7/site-packages (from matplotlib->spinalcordtoolbox===dev) (3.5.3) Collecting bz2file; python_version < "3.0" (from nibabel->spinalcordtoolbox===dev) Downloading https://files.pythonhosted.org/packages/61/39/122222b5e85cd41c391b68a99ee296584b2a2d1d233e7ee32b4532384f2d/bz2file-0.98.tar.gz Collecting sympy>=0.7.0 (from nipy->spinalcordtoolbox===dev) Using cached https://files.pythonhosted.org/packages/21/21/f4105795ca7f35c541d82c5b06be684dd2f5cb4f508fb487cd7aea4de776/sympy-1.4-py2.py3-none-any.whl Collecting contextlib2; python_version < "3.2" (from raven->spinalcordtoolbox===dev) Using cached https://files.pythonhosted.org/packages/a2/71/8273a7eeed0aff6a854237ab5453bc9aa67deb49df4832801c21f0ff3782/contextlib2-0.5.5-py2.py3-none-any.whl Requirement already satisfied: certifi>=2017.4.17 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2019.3.9) Requirement already satisfied: idna<2.9,>=2.5 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (2.6) Requirement already satisfied: chardet<3.1.0,>=3.0.2 in ./python/lib/python2.7/site-packages (from requests->spinalcordtoolbox===dev) (3.0.4) Requirement already satisfied: networkx>=1.8 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (2.2) Requirement already satisfied: pillow>=4.3.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (6.0.0) Requirement already satisfied: PyWavelets>=0.4.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.0.3) Requirement already satisfied: dask[array]>=1.0.0 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (1.2.0) Requirement already satisfied: cloudpickle>=0.2.1 in ./python/lib/python2.7/site-packages (from scikit-image->spinalcordtoolbox===dev) (0.8.1) Requirement already satisfied: mock>=2.0.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (2.0.0) Requirement already satisfied: wheel in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (0.29.0) Requirement already satisfied: backports.weakref>=1.0rc1 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0rc1) Collecting tensorflow-tensorboard<0.2.0,>=0.1.0 (from tensorflow==1.3.0->spinalcordtoolbox===dev) Using cached https://files.pythonhosted.org/packages/fb/34/14c23665a725c73932891e09b8f017a53aad545c9d5019d2817102dc5d9b/tensorflow_tensorboard-0.1.8-py2-none-any.whl Requirement already satisfied: protobuf>=3.3.0 in ./python/lib/python2.7/site-packages (from tensorflow==1.3.0->spinalcordtoolbox===dev) (3.7.1) Requirement already satisfied: pyOpenSSL>=0.14 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (17.0.0) Requirement already satisfied: cryptography>=1.3.4 in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (2.6.1) Requirement already satisfied: ipaddress in ./python/lib/python2.7/site-packages (from urllib3[secure]->spinalcordtoolbox===dev) (1.0.18) Requirement already satisfied: setuptools in ./python/lib/python2.7/site-packages (from kiwisolver>=1.0.1->matplotlib->spinalcordtoolbox===dev) (41.0.0) Collecting mpmath>=0.19 (from sympy>=0.7.0->nipy->spinalcordtoolbox===dev) Requirement already satisfied: decorator>=4.3.0 in ./python/lib/python2.7/site-packages (from networkx>=1.8->scikit-image->spinalcordtoolbox===dev) (4.4.0) Requirement already satisfied: toolz>=0.7.3; extra == "array" in ./python/lib/python2.7/site-packages (from dask[array]>=1.0.0->scikit-image->spinalcordtoolbox===dev) (0.9.0) Requirement already satisfied: funcsigs>=1; python_version < "3.3" in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.0.2) Requirement already satisfied: pbr>=0.11 in ./python/lib/python2.7/site-packages (from mock>=2.0.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (5.1.3) Requirement already satisfied: bleach==1.5.0 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (1.5.0) Requirement already satisfied: html5lib==0.9999999 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.9999999) Requirement already satisfied: werkzeug>=0.11.10 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (0.15.2) Requirement already satisfied: markdown>=2.6.8 in ./python/lib/python2.7/site-packages (from tensorflow-tensorboard<0.2.0,>=0.1.0->tensorflow==1.3.0->spinalcordtoolbox===dev) (2.6.11) Requirement already satisfied: enum34; python_version < "3" in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.1.6) Requirement already satisfied: asn1crypto>=0.21.0 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (0.22.0) Requirement already satisfied: cffi!=1.11.3,>=1.8 in ./python/lib/python2.7/site-packages (from cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (1.10.0) Requirement already satisfied: pycparser in ./python/lib/python2.7/site-packages (from cffi!=1.11.3,>=1.8->cryptography>=1.3.4->urllib3[secure]->spinalcordtoolbox===dev) (2.18) Building wheels for collected packages: dipy, bz2file Building wheel for dipy (setup.py) ... done Stored in directory: /Users/barryrl/Library/Caches/pip/wheels/35/2a/c7/10ee52be596c8fca26eaa5524b16da8aef72fabdf0c5606c10 Building wheel for bz2file (setup.py) ... done Stored in directory: /Users/barryrl/Library/Caches/pip/wheels/81/75/d6/e1317bf09bf1af5a30befc2a007869fa6e1f516b8f7c591cb9 Successfully built dipy bz2file Installing collected packages: h5py, keras-applications, keras-preprocessing, Keras, bz2file, nibabel, dipy, mpmath, sympy, nipy, contextlib2, raven, tqdm, transforms3d, portalocker, spinalcordtoolbox, tensorflow-tensorboard Running setup.py develop for spinalcordtoolbox Successfully installed Keras-2.2.4 bz2file-0.98 contextlib2-0.5.5 dipy-0.16.0 h5py-2.9.0 keras-applications-1.0.7 keras-preprocessing-1.0.9 mpmath-1.1.0 nibabel-2.4.0 nipy-0.4.2 portalocker-1.4.0 raven-6.10.0 spinalcordtoolbox sympy-1.4 tensorflow-tensorboard-0.1.8 tqdm-4.31.1 transforms3d-0.3.1 Checking if TensorFlow is working, if not attempting to install another version TensorFlow seems to be working. Checking if skimage is working, if not attempting work around it skimage seems to be working. Creating launchers for Python scripts... Installing binaries... >> . /Applications/SCT/ver_4_0_0_beta_2/python/bin/activate /Applications/SCT/ver_4_0_0_beta_2/python >> sct_download_data -d binaries_osx -o /Applications/SCT/ver_4_0_0_beta_2/bin /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Folder /Applications/SCT/ver_4_0_0_beta_2/bin has been created. Trying URL: https://osf.io/zjv4c/?action=download Downloading 20181204_sct_binaries_osx.tar.gz... Status: 100%|##########| 68.7M/68.7M [00:02<00:00, 30.7MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/bin Remove temporary file... Done! All requirements installed! >> . /Applications/SCT/ver_4_0_0_beta_2/python/bin/activate /Applications/SCT/ver_4_0_0_beta_2/python Installing data... >> rm -rf /Applications/SCT/ver_4_0_0_beta_2/data >> mkdir -p /Applications/SCT/ver_4_0_0_beta_2/data >> cd /Applications/SCT/ver_4_0_0_beta_2/data >> sct_download_data -d PAM50 /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/kc3jx/?action=download Downloading 20181214_PAM50.zip... Status: 100%|##########| 70.8M/70.8M [00:01<00:00, 41.0MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d gm_model /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/ugscu/?action=download Downloading 20160922_gm_model.zip... Status: 100%|##########| 10.3M/10.3M [00:00<00:00, 26.9MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d optic_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/g4fwn/?action=download Downloading 20170413_optic_models.zip... Status: 100%|##########| 17.7k/17.7k [00:00<00:00, 15.0MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d pmj_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/4gufr/?action=download Downloading 20170922_pmj_models.zip... Status: 100%|##########| 8.87k/8.87k [00:00<00:00, 7.44MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d deepseg_sc_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/avf97/?action=download Downloading 20180610_deepseg_sc_models.zip... Status: 100%|##########| 58.7M/58.7M [00:03<00:00, 18.6MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d deepseg_gm_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/b9y4x/?action=download Downloading 20180205_deepseg_gm_models.zip... Status: 100%|##########| 2.28M/2.28M [00:00<00:00, 8.29MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d deepseg_lesion_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/eg7v9/?action=download Downloading 20180613_deepseg_lesion_models.zip... Status: 100%|##########| 16.0M/16.0M [00:01<00:00, 8.20MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! >> sct_download_data -d c2c3_disc_models /Applications/SCT/ver_4_0_0_beta_2/python/lib/python2.7/site-packages/cryptography/hazmat/primitives/constant_time.py:26: CryptographyDeprecationWarning: Support for your Python version is deprecated. The next version of cryptography will remove support. Please upgrade to a 2.7.x release that supports hmac.compare_digest as soon as possible. utils.PersistentlyDeprecated2018, Trying URL: https://osf.io/t97ap/?action=download Downloading 20190117_c2c3_disc_models.zip... Status: 100%|##########| 8.94k/8.94k [00:00<00:00, 8.03MB/s] Check if folder already exists... Unzip data to: /Applications/SCT/ver_4_0_0_beta_2/data Remove temporary file... Done! Do you want to add the sct_* scripts to your PATH environment? [y]es/[n]o: y Validate installation... SCT info: - version: dev - path: /Applications/SCT/ver_4_0_0_beta_2 OS: osx (Darwin-16.7.0-x86_64-i386-64bit) CPU cores: Available: 8, Used by SCT: 8 RAM: Primary memory available: 16.00 gigabytes Check Python executable.............................[OK] Using bundled python 2.7.3 |Continuum Analytics, Inc.| (default, Dec 20 2012, 09:57:39) [GCC 4.0.1 (Apple Inc. build 5493)] at /Applications/SCT/ver_4_0_0_beta_2/python/bin/python Check if data are installed.........................[OK] Check if Keras is installed.........................[OK] (2.2.4) Check if dipy is installed..........................[OK] (0.16.0) Check if futures is installed.......................[OK] Check if h5py is installed..........................[OK] (2.9.0) Check if matplotlib is installed....................[OK] (2.2.3) Check if nibabel is installed.......................[OK] (2.4.0) Check if nipy is installed..........................[OK] (0.4.2) Check if pandas is installed........................[OK] (0.23.4) Check if psutil is installed........................[OK] (5.6.1) Check if raven is installed.........................[OK] Check if requests is installed......................[OK] (2.21.0) Check if numpy is installed.........................[OK] (1.11.3) Check if scipy is installed.........................[OK] (1.2.1) Check if scikit-image is installed..................[OK] (0.14.2) Check if scikit-learn (0.17.1) is installed.........[OK] Check if tensorflow (1.3.0) is installed............[OK] Check if xlrd is installed..........................[OK] (1.2.0) Check if xlutils is installed.......................[OK] Check if xlwt is installed..........................[OK] (1.3.0) Check if tqdm is installed..........................[OK] (4.31.1) Check if transforms3d is installed..................[OK] (0.3.1) Check if urllib3[secure] is installed...............[OK] (1.24.1) Check if portalocker is installed...................[OK] (1.4.0) Check if spinalcordtoolbox is installed.............[OK] Check ANTs compatibility with OS ...................[FAIL] Create temporary folder (/var/folders/mf/5wv63z61295dcfvzm_l2llh8003jn9/T/sct-20190416092756.783148-test_ants-8zvYsu)... Traceback (most recent call last): File "/Applications/SCT/ver_4_0_0_beta_2/scripts/isct_test_ants.py", line 181, in main() File "/Applications/SCT/ver_4_0_0_beta_2/scripts/isct_test_ants.py", line 82, in main printv('\nEstimate rigid transformation between paired landmarks...', verbose) File "/Applications/SCT/ver_4_0_0_beta_2/scripts/isct_test_ants.py", line 148, in printv logger.info(string) NameError: global name 'logger' is not defined Check PropSeg compatibility with OS ................[OK] Check if figure can be opened.......................[OK] Installation validation NG! Please copy the historic of this Terminal (starting with the command install_sct) and paste it in the SCT Help forum under a new ticket: https://sourceforge.net/p/spinalcordtoolbox/discussion/help/ Installation failed